|Class||Analysis and data manipulation command|
|Arguments||<codominant marker> [<allele dose estimate>] [mcmc]|
Gives iterative peeling or MCMC (Markov Chain Monte-Carlo) estimates of the genotype probability estimates for the given marker for each individual: a vector of probabilities corresponding to the possible genotypes at that marker. For an observed genotype, this is 100% for the observed value and 0% for all other possible genotype values. For an unobserved genotype, it gives the probability distribution of possible genotypes conditional on the sample allele frequencies (assuming Hardy-Weinberg Equilibrium) and the observed genotypes in the individual's relatives. Estimation is carried out by iterative peeling or using Sib-pair's single locus genotype MCMC sampler (hybrid Metropolis-Gibbs).
If the name of an extant quantitative trait is appended to the command, the expected gene dose for the first (ie lowest in the collation order) allele will be written to this variable. These estimates can then be used for association analysis.
The gpe command respects the set frequencies command, so that the population allele frequencies can be specified in advance. This allows appropriate estimation in samples ascertained on genotypes at the locus to be tested. The obvious use of this is in kin-cohort or counselling type analyses.
If inbreeding loops are present in the pedigree, the iterative peeling approach is only approximate: loops are (effectively) broken in an unusual fashion (see Wang et al ).
>> include williamsex.in >> set freq ldl 0.999 0.001 >> gpe ldl >> set loc dose qua >> gpe ldl dose >> dose=2-dose; if (dose < 0) then dose=0 >> write
|set frequencies||Specify allele frequencies|
|set analysis||Include imputed genotypes in association analysis|
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